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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ), 'gf_id' => 'HOM05D001098', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001098' ), 'data_identifier' => 'HOM05D001098', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001098', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '558', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03220' => 'bna', 'A03p24140' => 'bna', 'A03p63540' => 'bna', 'A03p65600' => 'bna', 'A04p02190' => 'bna', 'A04p14920' => 'bna', 'A04p32520' => 'bna', 'A08p21890' => 'bna', 'A09p10750' => 'bna', 'A09p51630' => 'bna', 'Aa31LG10G13690' => 'aar', 'Aa31LG1G25050' => 'aar', 'Aa31LG9G370' => 'aar', 'Aa31sc18G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2168' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.665' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1241' => 'aag', 'Actinidia10106' => 'ach', 'Actinidia11309' => 'ach', 'Actinidia17990' => 'ach', 'Actinidia20200' => 'ach', 'Actinidia20579' => 'ach', 'Actinidia22712' => 'ach', 'Actinidia34622' => 'ach', 'Actinidia35960' => 'ach', 'Actinidia39858' => 'ach', 'Ah.01g017660' => 'amhyb', 'Ah.12g052240' => 'amhyb', 'Ah.13g072980' => 'amhyb', 'AL4G41900' => 'aly', 'AL5G41220' => 'aly', 'AL7G15820' => 'aly', 'AL7G47530' => 'aly', 'Aqoxy1G01619' => 'aox', 'Aqoxy2G01309' => 'aox', 'Aqoxy2G04114' => 'aox', 'Aqoxy3G04159' => 'aox', 'Aqoxy5G04128' => 'aox', 'Aqoxy6G01547' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1X8DY6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U49GI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.74EJA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7NF1VE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZHK7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZV8JK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N1X7B2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SLE9L7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UD8U5Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W5G0Q3' => 'arhy', 'AT2G43240' => 'ath', 'AT3G59360' => 'ath', 'AT5G41760' => 'ath', 'ATR0057G016' => 'atr', 'ATR0743G220' => 'atr', 'ATR0796G272' => 'atr', 'Atru.chr3.1600' => 'acertr', 'Atru.chr3.1608' => 'acertr', 'Atru.chr5.3569' => 'acertr', 'Atru.chr9.2056' => 'acertr', 'AUR62002604' => 'cqu', 'AUR62010182' => 'cqu', 'AUR62010803' => 'cqu', 'AUR62013184' => 'cqu', 'AUR62019800' => 'cqu', 'AUR62030022' => 'cqu', 'BcaB01g03402' => 'bca', 'BcaB02g07472' => 'bca', 'BcaB02g08225' => 'bca', 'BcaB03g12410' => 'bca', 'BcaB06g27663' => 'bca', 'BcaB06g29292' => 'bca', 'BcaC01g00493' => 'bca', 'BcaC01g05248' => 'bca', 'BcaC02g07198' => 'bca', 'BcaC02g08931' => 'bca', 'BcaC02g10053' => 'bca', 'BcaC04g22135' => 'bca', 'BcaC07g40278' => 'bca', 'BcaC07g40460' => 'bca', 'BcaC08g44442' => 'bca', 'BcaC08g44870' => 'bca', 'BcaNung02390' => 'bca', 'BcaNung04604' => 'bca', 'BcaNung06457' => 'bca', 'BolC1t00346H' => 'bol', 'BolC1t00347H' => 'bol', 'BolC1t02142H' => 'bol', 'BolC3t14466H' => 'bol', 'BolC3t15235H' => 'bol', 'BolC3t18723H' => 'bol', 'BolC3t20307H' => 'bol', 'BolC4t24909H' => 'bol', 'BolC4t26481H' => 'bol', 'BolC4t28525H' => 'bol', 'BolC6t37638H' => 'bol', 'BolC7t46536H' => 'bol', 'BolC7t46537H' => 'bol', 'BolC8t51041H' => 'bol', 'BraA01t00307Z' => 'bra', 'BraA02t07250Z' => 'bra', 'BraA03t11624Z' => 'bra', 'BraA03t15424Z' => 'bra', 'BraA03t15613Z' => 'bra', 'BraA04t15948Z' => 'bra', 'BraA04t17130Z' => 'bra', 'BraA04t18716Z' => 'bra', 'BraA07t28272Z' => 'bra', 'BraA08t32553Z' => 'bra', 'BraA08t34142Z' => 'bra', 'BraA09t40603Z' => 'bra', 'BraA10t45200Z' => 'bra', 'C01p03570' => 'bna', 'C01p22110' => 'bna', 'C03p20580' => 'bna', 'C03p28730' => 'bna', 'C03p58210' => 'bna', 'C03p62850' => 'bna', 'C03p64650' => 'bna', 'C03p80640' => 'bna', 'C04p22260' => 'bna', 'C04p33450' => 'bna', 'C04p48990' => 'bna', 'C04p70210' => 'bna', 'C06p24840' => 'bna', 'C07p57770' => 'bna', 'C07p61120' => 'bna', 'C07p61130' => 'bna', 'C08p34400' => 'bna', 'C09p31930' => 'bna', 'CAN.G321.13' => 'can', 'CAN.G321.15' => 'can', 'CAN.G710.62' => 'can', 'CAN.G986.41' => 'can', 'CANSAT25G0204' => 'cansat', 'CANSAT54G1180' => 'cansat', 'CARHR138320' => 'chi', 'CARHR169740' => 'chi', 'CARHR169750' => 'chi', 'CARHR212820' => 'chi', 'CARHR243660' => 'chi', 'Carub.0004s2571' => 'cru', 'Carub.0005s2609' => 'cru', 'Carub.0007s0496' => 'cru', 'Carub.0007s3364' => 'cru', 'Carub.0007s3368' => 'cru', 'Ca_04727_v3' => 'car', 'Ca_05517_v3' => 'car', 'Ca_06505_v3' => 'car', 'Ca_07098_v3' => 'car', 'Ca_09495_v3' => 'car', 'Ca_11404_v3' => 'car', 'Ca_27647_v3' => 'car', 'Ca_30098_v3' => 'car', 'CBR_g17781' => 'cbr', 'CBR_g17783' => 'cbr', 'CBR_g32154' => 'cbr', 'CBR_g38158' => 'cbr', 'Cc02_g38980' => 'ccan', 'Cc09_g04080' => 'ccan', 'Cc09_g10880' => 'ccan', 'CDE04G3071' => 'cde', 'CDE08G0816' => 'cde', 'CDE10G0149' => 'cde', 'Cfa006231' => 'cfa', 'Cfa012849' => 'cfa', 'Cfa015774' => 'cfa', 'Ciclev10011853m.g' => 'ccl', 'Ciclev10020426m.g' => 'ccl', 'Ciclev10021053m.g' => 'ccl', 'Ciclev10028748m.g' => 'ccl', 'CiPaw.01G102500' => 'cil', 'CiPaw.05G093900' => 'cil', 'CiPaw.06G114700' => 'cil', 'CiPaw.08G112200' => 'cil', 'CiPaw.11G124400' => 'cil', 'CiPaw.12G085200' => 'cil', 'ClCG02G010830' => 'cla', 'ClCG08G003850' => 'cla', 'ClCG08G004290' => 'cla', 'COL.COLO4_06326' => 'col', 'COL.COLO4_06327' => 'col', 'COL.COLO4_14417' => 'col', 'COL.COLO4_23115' => 'col', 'COL.COLO4_34319' => 'col', 'Cpa.g.sc122.28' => 'cpa', 'Cpa.g.sc1440.1' => 'cpa', 'Cpa.g.sc2328.1' => 'cpa', 'Cpa.g.sc71.26' => 'cpa', 'Cre02.g095107' => 'cre', 'Cre02.g095109' => 'cre', 'CsaV3_6G003740' => 'csa', 'CsaV3_6G003980' => 'csa', 'CsaV3_6G010050' => 'csa', 'CSS0007326' => 'camsi', 'CSS0016031' => 'camsi', 'CSS0017763' => 'camsi', 'CSS0028273' => 'camsi', 'CSS0035152' => 'camsi', 'CSS0035199' => 'camsi', 'CSS0035352' => 'camsi', 'CSS0044943' => 'camsi', 'DCAR_006385' => 'dca', 'DCAR_006386' => 'dca', 'DCAR_006966' => 'dca', 'DCAR_008651' => 'dca', 'DCAR_027528' => 'dca', 'DCAR_029924' => 'dca', 'Dinv21354' => 'din', 'Dinv22694' => 'din', 'Dinv32556' => 'din', 'Dinv36402' => 'din', 'Dinv37554' => 'din', 'Dinv41864' => 'din', 'Dinv43895' => 'din', 'Dinv44216' => 'din', 'Duzib093G0299' => 'dzi', 'Duzib106G0563' => 'dzi', 'Duzib128G1666' => 'dzi', 'Duzib132G1111' => 'dzi', 'Duzib248G0955' => 'dzi', 'ECA233G3688' => 'eca', 'ECA233G5431' => 'eca', 'ECA234G3902' => 'eca', 'EL10Ac3g06301' => 'bvu', 'EL10Ac5g12877' => 'bvu', 'EL10Ac9g21546' => 'bvu', 'Eucgr.A00254' => 'egr', 'Eucgr.E00839' => 'egr', 'Eucgr.H00419' => 'egr', 'Eucgr.I01538' => 'egr', 'FAN02G0075' => 'fan', 'FAN02G0815' => 'fan', 'FAN02G3857' => 'fan', 'FAN04G0784' => 'fan', 'FAN07G1473' => 'fan', 'FAN08G0493' => 'fan', 'FAN13G0365' => 'fan', 'FAN15G1608' => 'fan', 'FAN17G2346' => 'fan', 'FAN18G3402' => 'fan', 'FAN24G1038' => 'fan', 'FAN27G2361' => 'fan', 'FvH4_2g16930' => 'fve', 'FvH4_4g11380' => 'fve', 'FvH4_5g03970' => 'fve', 'Glyma.02G312000' => 'gma', 'Glyma.03G255900' => 'gma', 'Glyma.10G296000' => 'gma', 'Glyma.14G000600' => 'gma', 'Glyma.19G253600' => 'gma', 'Glyma.20G246100' => 'gma', 'Gohir.A01G095201' => 'ghi', 'Gohir.A04G048165' => 'ghi', 'Gohir.A04G111700' => 'ghi', 'Gohir.A08G227500' => 'ghi', 'Gohir.A09G059050' => 'ghi', 'Gohir.A11G094900' => 'ghi', 'Gohir.A11G329800' => 'ghi', 'Gohir.A12G104501' => 'ghi', 'Gohir.A12G110900' => 'ghi', 'Gohir.A13G064400' => 'ghi', 'Gohir.D04G152000' => 'ghi', 'Gohir.D08G247900' => 'ghi', 'Gohir.D08G275200' => 'ghi', 'Gohir.D11G099900' => 'ghi', 'Gohir.D11G349000' => 'ghi', 'Gohir.D12G114200' => 'ghi', 'Gohir.D13G099800' => 'ghi', 'Gorai.004G264400' => 'gra', 'Gorai.004G293600' => 'gra', 'Gorai.007G106100' => 'gra', 'Gorai.007G379300' => 'gra', 'Gorai.008G123700' => 'gra', 'Gorai.012G138800' => 'gra', 'Gorai.013G064700' => 'gra', 'Gorai.013G111800' => 'gra', 'GSVIVG01002623001' => 'vvi', 'GSVIVG01003756001' => 'vvi', 'GSVIVG01013580001' => 'vvi', 'GSVIVG01014888001' => 'vvi', 'GSVIVG01023429001' => 'vvi', 'GSVIVG01023430001' => 'vvi', 'GSVIVG01023864001' => 'vvi', 'GSVIVG01027052001' => 'vvi', 'HanXRQChr02g0057871' => 'han', 'HanXRQChr05g0160081' => 'han', 'HanXRQChr07g0185971' => 'han', 'HanXRQChr07g0186261' => 'han', 'HanXRQChr07g0190411' => 'han', 'HanXRQChr09g0258101' => 'han', 'HanXRQChr11g0353061' => 'han', 'HanXRQChr14g0432591' => 'han', 'HanXRQChr16g0515181' => 'han', 'Haze_00096' => 'cav', 'Haze_00721' => 'cav', 'Haze_01974' => 'cav', 'Haze_04603' => 'cav', 'Haze_08676' => 'cav', 'Haze_10071' => 'cav', 'Haze_26352' => 'cav', 'Haze_26763' => 'cav', 'Hma1.2p1_0032F.1_g018710' => 'hma', 'Hma1.2p1_0077F.1_g039790' => 'hma', 'Hma1.2p1_0271F.1_g108730' => 'hma', 'Hma1.2p1_0597F.1_g186470' => 'hma', 'Hma1.2p1_0952F.1_g240870' => 'hma', 'Hma1.2p1_2900F.1_g330040' => 'hma', 'HPP92_003579' => 'vpl', 'HPP92_015755' => 'vpl', 'HPP92_024019' => 'vpl', 'Hund06357' => 'sun', 'Hund12228' => 'sun', 'Hund22601' => 'sun', 'Lalb_Chr02g0144331' => 'lal', 'Lalb_Chr04g0261781' => 'lal', 'Lalb_Chr06g0164491' => 'lal', 'Lalb_Chr10g0107701' => 'lal', 'Lalb_Chr21g0307611' => 'lal', 'Lj1g0005672' => 'lja', 'Lj3A231G6' => 'lonja', 'Lj5g0027220' => 'lja', 'Lj6C60G7' => 'lonja', 'Lj7A503T49' => 'lonja', 'Lj9A408T81' => 'lonja', 'Lj9C592G6' => 'lonja', 'LjContig00081g0022408' => 'lja', 'Lsat_1_v5_gn_1_104560' => 'lsa', 'Lsat_1_v5_gn_1_71640' => 'lsa', 'Lsat_1_v5_gn_2_51900' => 'lsa', 'Lsat_1_v5_gn_2_62200' => 'lsa', 'Lsat_1_v5_gn_3_139161' => 'lsa', 'Lsat_1_v5_gn_3_40300' => 'lsa', 'Lsat_1_v5_gn_5_58180' => 'lsa', 'Lsat_1_v5_gn_5_70220' => 'lsa', 'Lsat_1_v5_gn_6_55000' => 'lsa', 'Lsat_1_v5_gn_7_70641' => 'lsa', 'Lsat_1_v5_gn_8_120701' => 'lsa', 'Lsat_1_v5_gn_9_124300' => 'lsa', 'Manes.02G013500' => 'mes', 'Manes.02G204100' => 'mes', 'Manes.05G025700' => 'mes', 'Manes.11G116200' => 'mes', 'Manes.12G001900' => 'mes', 'Manes.13G001200' => 'mes', 'Manes.18G113200' => 'mes', 'Mapoly0012s0161' => 'mpo', 'Mapoly0165s0011' => 'mpo', 'MBI01_g17242_MAGBIO' => 'mbi', 'MBI01_g32424_MAGBIO' => 'mbi', 'MBI04_g31202_MAGBIO' => 'mbi', 'MBI08_g46113_MAGBIO' => 'mbi', 'MBI11_g35031_MAGBIO' => 'mbi', 'MBI17_g17491_MAGBIO' => 'mbi', 'MCO03G533' => 'mco', 'MCO11G347' => 'mco', 'MCO13G512' => 'mco', 'MCO17G012' => 'mco', 'MCO17G031' => 'mco', 'MD04G1037800' => 'mdo', 'MD05G1140500' => 'mdo', 'MD05G1141000' => 'mdo', 'MD06G1101100' => 'mdo', 'MD11G1242300' => 'mdo', 'MD13G1273000' => 'mdo', 'MD14G1120800' => 'mdo', 'Medtr1g116565' => 'mtr', 'Medtr5g099280' => 'mtr', 'Medtr7g117060' => 'mtr', 'MELO3C011623.2' => 'cme', 'MELO3C011675.2' => 'cme', 'MELO3C013485.2' => 'cme', 'Migut.B00005' => 'egut', 'Migut.B01836' => 'egut', 'Migut.G01025' => 'egut', 'MSTRG.16957' => 'ama', 'MSTRG.20886' => 'ama', 'MSTRG.21995' => 'ama', 'MSTRG.24584' => 'ama', 'Nitab4.5_0000305g0120' => 'nta', 'Nitab4.5_0000978g0130' => 'nta', 'Nitab4.5_0001003g0090' => 'nta', 'Nitab4.5_0001003g0120' => 'nta', 'Nitab4.5_0001049g0120' => 'nta', 'Nitab4.5_0002466g0040' => 'nta', 'Nitab4.5_0002908g0090' => 'nta', 'Nitab4.5_0009631g0030' => 'nta', 'Nitab4.5_0012793g0010' => 'nta', 'Nitab4.5_0013597g0010' => 'nta', 'Nn1g01805' => 'nnu', 'Nn1g09874' => 'nnu', 'Nn3g19085' => 'nnu', 'Nn6g31647' => 'nnu', 'Nn7g37649' => 'nnu', 'Oeu007848.1' => 'oeu', 'Oeu012219.1' => 'oeu', 'Oeu034469.1' => 'oeu', 'Oeu050440.1' => 'oeu', 'Oeu053845.1' => 'oeu', 'Os01g0898900' => 'osa', 'Os02g0604300' => 'osa', 'Os04g0490600' => 'osa', 'Os06g0523400' => 'osa', 'Os07g0573700' => 'osa', 'Peaxi162Scf00024g00327' => 'pax', 'Peaxi162Scf00241g00220' => 'pax', 'Peaxi162Scf00286g00116' => 'pax', 'Peaxi162Scf00296g01213' => 'pax', 'Peaxi162Scf00296g01214' => 'pax', 'Peaxi162Scf00323g00718' => 'pax', 'Peaxi162Scf01012g00019' => 'pax', 'PGR042G3574' => 'pgr', 'PGR083G2776' => 'pgr', 'PGR142G0121' => 'pgr', 'PGR142G3259' => 'pgr', 'PGSC0003DMG400000209' => 'stu', 'PGSC0003DMG400016250' => 'stu', 'PGSC0003DMG400021614' => 'stu', 'Phvul.006G110600' => 'pvu', 'Phvul.007G003900' => 'pvu', 'Phvul.008G292800' => 'pvu', 'Potri.001G094600' => 'ptr', 'Potri.003G136800' => 'ptr', 'Potri.008G077300' => 'ptr', 'Potri.010G180500' => 'ptr', 'Potri.016G113200' => 'ptr', 'Potri.017G035800' => 'ptr', 'Pp3c10_200' => 'ppa', 'Pp3c14_2280' => 'ppa', 'Pp3c5_28860' => 'ppa', 'PRCOL_00001440' => 'pco', 'PRCOL_00001790' => 'pco', 'PRCOL_00005838' => 'pco', 'Prupe.1G187700' => 'ppe', 'Prupe.5G114600' => 'ppe', 'Prupe.8G181000' => 'ppe', 'Psat2g000520' => 'psa', 'Psat3g003160' => 'psa', 'Psat6g241560' => 'psa', 'PSO017G5825' => 'pso', 'PSO063G3657' => 'pso', 'PSO170G1456' => 'pso', 'PSO423G0206' => 'pso', 'PSO541G0403' => 'pso', 'PSO675G1128' => 'pso', 'PSO675G9097' => 'pso', 'QL02p031530' => 'qlo', 'QL02p031533' => 'qlo', 'QL02p032313' => 'qlo', 'QL04p058262' => 'qlo', 'QL04p059398' => 'qlo', 'QL05p059688' => 'qlo', 'QL05p062032' => 'qlo', 'QL05p062370' => 'qlo', 'QL06p014336' => 'qlo', 'QL10p047425' => 'qlo', 'QL10p056053' => 'qlo', 'QL11p009150' => 'qlo', 'RcHm_v2.0_Chr4g0407851' => 'rch', 'RcHm_v2.0_Chr6g0281071' => 'rch', 'RcHm_v2.0_Chr6g0281091' => 'rch', 'RcHm_v2.0_Chr6g0281101' => 'rch', 'RcHm_v2.0_Chr7g0195531' => 'rch', 'Rhsim02G0075800' => 'rsi', 'Rhsim05G0044700' => 'rsi', 'Rhsim07G0006600' => 'rsi', 'Rhsim07G0084500' => 'rsi', 'Sabra03G0098300' => 'sbr', 'Sabra03G0098400' => 'sbr', 'Sabra08G0057600' => 'sbr', 'Sabra17G0022700' => 'sbr', 'SalBow1G7648' => 'sbo', 'SalBow3G4600' => 'sbo', 'SalBow7G2674' => 'sbo', 'Sc01g0010110' => 'sci', 'Sc08g0002100' => 'sci', 'Sc19g0002170' => 'sci', 'Sed0001161' => 'sed', 'Sed0004441' => 'sed', 'Sed0022439' => 'sed', 'Sed0023457' => 'sed', 'Sed0023927' => 'sed', 'SEGI_01030' => 'sgi', 'SEGI_03538' => 'sgi', 'SEGI_11233' => 'sgi', 'SEGI_11600' => 'sgi', 'SEGI_20595' => 'sgi', 'SEGI_22114' => 'sgi', 'SEGI_30986' => 'sgi', 'SEGI_32505' => 'sgi', 'SEGI_39364' => 'sgi', 'SGA_v2.0_scaffold12G06145' => 'sas', 'SGA_v2.0_scaffold17G08059' => 'sas', 'SGA_v2.0_scaffold5G02988' => 'sas', 'SHI13106' => 'shi', 'SHI27585' => 'shi', 'SMO118G0063' => 'smo', 'SMO141G0118' => 'smo', 'Solyc01g095540.3' => 'sly', 'Solyc09g098520.4' => 'sly', 'Solyc11g008590.2' => 'sly', 'Solyc11g008610.3' => 'sly', 'Sopen01g039290' => 'spe', 'Sopen09g036440' => 'spe', 'Sopen11g004380' => 'spe', 'Sopen11g004400' => 'spe', 'Sp4g25370' => 'spa', 'Sp5g03760' => 'spa', 'Sp7g33130' => 'spa', 'TAR362G0247' => 'tar', 'TAR375G0190' => 'tar', 'TAR381G1518' => 'tar', 'TAR383G0595' => 'tar', 'TAR629G1890' => 'tar', 'TAR633G0110' => 'tar', 'TAR636G1838' => 'tar', 'TAR664G0001' => 'tar', 'THA.LOC104802300' => 'tha', 'THA.LOC104803609' => 'tha', 'THA.LOC104823607' => 'tha', 'Thecc.01G347100' => 'tca', 'Thecc.02G147100' => 'tca', 'Thecc.05G002800' => 'tca', 'Thecc.05G185000' => 'tca', 'Thhalv10001470m.g' => 'esa', 'Thhalv10006015m.g' => 'esa', 'Thhalv10025582m.g' => 'esa', 'Thhalv10027829m.g' => 'esa', 'TPR.G10392' => 'tpr', 'TPR.G18630' => 'tpr', 'TPR.G5344' => 'tpr', 'TWI18G0847' => 'twi', 'TWI23G1043' => 'twi', 'TWI36G1504' => 'twi', 'TWI75G1677' => 'twi', 'TWI79G1444' => 'twi', 'unitig_18.g30045' => 'ugi', 'unitig_578.g16267' => 'ugi', 'unitig_578.g16268' => 'ugi', 'unitig_8.g4799' => 'ugi', 'unitig_90.g27539' => 'ugi', 'vmacro02343' => 'vma', 'vmacro13191' => 'vma', 'vmacro13917' => 'vma', 'vmacro15641' => 'vma', 'VMungo0540G0619' => 'vmu', 'VMungo0540G2158' => 'vmu', 'VMungo0647G1767' => 'vmu', 'VMungo0647G1862' => 'vmu', 'VMungo0720G2121' => 'vmu', 'VMungo0720G2916' => 'vmu', 'Zm00001eb137090' => 'zma', 'Zm00001eb184070' => 'zma', 'Zm00001eb241050' => 'zma', 'Zm00001eb246560' => 'zma', 'Zm00001eb325140' => 'zma', 'Zm00001eb365640' => 'zma', 'Zm00001eb382810' => 'zma', 'Zm00001eb412040' => 'zma' ) $gf_id = 'HOM05D001098' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001098' ) $data_identifier = 'HOM05D001098' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 19, 'bol' => (int) 14, 'bra' => (int) 13, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 8, 'han' => (int) 9, 'cav' => (int) 8, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 12, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 5, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 12, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb412040' $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